7-10241816-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.116 in 151,712 control chromosomes in the GnomAD database, including 1,896 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1896 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.744
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.116
AC:
17579
AN:
151594
Hom.:
1892
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.221
Gnomad AMR
AF:
0.0421
Gnomad ASJ
AF:
0.0344
Gnomad EAS
AF:
0.0619
Gnomad SAS
AF:
0.0808
Gnomad FIN
AF:
0.0578
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0494
Gnomad OTH
AF:
0.0835
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.116
AC:
17602
AN:
151712
Hom.:
1896
Cov.:
32
AF XY:
0.114
AC XY:
8443
AN XY:
74186
show subpopulations
Gnomad4 AFR
AF:
0.285
Gnomad4 AMR
AF:
0.0420
Gnomad4 ASJ
AF:
0.0344
Gnomad4 EAS
AF:
0.0613
Gnomad4 SAS
AF:
0.0807
Gnomad4 FIN
AF:
0.0578
Gnomad4 NFE
AF:
0.0494
Gnomad4 OTH
AF:
0.0826
Alfa
AF:
0.0498
Hom.:
162
Bravo
AF:
0.121
Asia WGS
AF:
0.0730
AC:
255
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
3.0
DANN
Benign
0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7785107; hg19: chr7-10281443; API